The effect of solar disinfection on the viability of intestinal protozoa Giardia lamblia, Microsporidia sp., Cryptosporidium parvum, Cyclospora cyatenensis and Entamoeba histolytica in drinking water was studied as compared to chlorine disinfection. The protozoa were collected from stool samples, to infect to the distilled water. Chlorinated water samples were prepared at concentration of 4 ppm, and the parasites were incubated overnight at room temperature with the treated water. Sun treatment was applied for 2 exposures (6 & 24 hrs), in summer and winter. Sun treated water samples were put in tubes and exposed to sun. The 2 disinfection methods were tested in plastic and glass test tubes. Parasites viability was assessed by viability assay using trypan blue stain (0.4%), and bioassay infectivity tests in experimentally laboratory bred mice. Results proved that all parasites' viability was not affected by chlorine, following solar disinfection treatment, parasites became dark blue in colour and deformed by trypan blue stain. High parasites death was recorded for all parasites except Microsporidia sp. Bioassay infectivity test showed a statistically significant reduction in mean number of all parasites in intestinal sections compared to controls. The best results were tubes exposure to sun for 24 hrs in summer, where G. lamblia, C. parvum and C. cyatenensis were inactivated or absence in intestinal sections. No statistically significant difference was between the use of plastic and glass tubes, either in chlorine or sun treated parasites. So, solar disinfection proved a simple, cheap and effective means for improving water for human use, particularly in developing countries.